Chen, Yun-Ru Ruby

ChenYR.jpgAssociate Research Fellow

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Telephone: +886-2-27871275




  • B.S., Agricultural Chemistry, National Taiwan University, 1996
  • Ph.D., Molecular and Structural Biochemistry, North Carolina State University, 2003
  • Postdoctoral Researcher, Molecular Biology and Biochemistry, University of California at Irvine, 2004-2006
  • Postdoctoral Researcher, The Genomics Research Center, Academia Sinica, 2006-2007
  • Assistant Research Fellow, The Genomics Research Center, Academia Sinica, 2007-2014
  • Associate Research Fellow, The Genomics Research Center, Academia Sinica, 2014-present


  • Ta-You Wu Memorial Award, 2015
  • TWAS Young Affiliate, East & Southeast Asia and Pacific Region, 2015-2019
  • The 13th Y.Z. Hsu Scientific Paper Award, 2015
  • Academia Sinica Research Award for Junior Research Investigators, 2015
  • Junior Faculty Award, the 12th International Conference on Alzheimer’s Disease and Parkinson’s Disease, 2015
  • Promising Women in Science Award, Wu Chieh Shiung Education Foundation, 2014
  • Young Investigator Award, Biophysical Society of R.O.C., 2013 
  • Taiwan Dementia Society, LiFu Medical Research Foundation Academic Award, Advisor of the 1st Price, 2012, and 2nd Price, 2011
  • The Taiwan Society for Biochemistry and Molecular Biology Traveling Fellowship, 2012
  • Academia Sinica Postdoctoral Fellowship, 2006-2007



Protein Folding/Misfolding, Amyloids, and Neurodegenerative Diseases

My research focuses on understanding the mechanism of protein misfolding diseases, amyloidosis, by various techniques including biochemical, biophysical, molecular, and cellular methods. Our long-term goal is to elucidate the disease mechanisms of amyloidoses with the aspects of protein folding and structure, pathogenic protein interactions, and relate the results to the medical consequences. We further utilize the knowledge to develop novel diagnostic and therapeutic means. Many ageing-related neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and Huntington’s disease (HD) belong to amyloidosis. Amyloidosis is caused by aggregation of misfolded proteins to form amyloid fibrils comprised of specific cross-β structures. Amyloid oligomers that existed in several neurodegenerative diseases imply a common toxicity mechanism in different neurodegenerative diseases. Currently, we are working on several amyloids and their interacting partners in the neurodegenerative diseases including amyloid-β (Aβ) and tau, the main constituents of senile plaques and tangles, in AD, α-synuclein, the component of Lewy bodies in PD, and TDP-43, a novel inclusion found in a subtype of frontotemporal lobar dementia (FTLD-U) and amyotrophic lateral sclerosis (ALS). We start from elucidating structural conversion and aggregation mechanism of such aggregation and further develop their antibodies and small molecule inhibitors. Moreover, we investigate the glycosylation effect on these proteins and interacting partners. The major research interests are listed as follows:

  • Protein folding and misfolding of amyloids in neurodegenerative diseases.
  • Amyloid protein oligomerization and the toxicity mechanisms in neurodegenerative diseases.
  • Amyloid modifiers and glycosylation effect.
  • Drug screening, diagnostic, and therapeutic developments in neurodegenerative diseases.

Amyloid formation, a detrimental protein aggregation, is initiated by protein 
misfolding followed by self-association to ultimately form amyloid fibrils.
The discovery of cytotoxic pre-fibrillar oligomers in many neurodegenerative 
diseases underscores the importance of understanding the folding, aggregation,
and pathogenic mechanisms as well as developing diagnostic and therapeutic



  • Yu-Jen Chang, U-Ser Jeng, Ya-Ling Chiang, Ing-Shouh Hwang, and Yun-Ru Chen*, accepted, “Glycine-Alanine Dipeptide Repeat from C9orf72 Hexanucleotide Expansions Forms Toxic Amyloids Possessing Cell-to-cell Transmission Property”, Journal of Biological Chemistry. (SCI)
  • Patricia F. Kao, Yun-Ru Chen, Xiao-Bo Liu, Charles DeCarli, William W. Seeley, and Lee-Way Jin*, 2015, “Detection of TDP-43 oligomers in frontotemporal lobar degeneration-TDP”, ANNALS OF NEUROLOGY, 78(2), 211-221. (SCI)
  • Yu-Jen Chang, Yun-Ru Chen*, 2014, “The Co-existence of an Equal Amount of Alzheimer’s Amyloid-β 40 and 42 forms Structurally Stable and Toxic Oligomers through a Distinct Pathway”, FEBS JOURNAL, 281(11), 2674-2687. (SCI)
  • Huei-Jyuan Pan, Ruei-Lin Wang, Jian-Long Xiao, Yu-Jen Chang, Ji-Yen Cheng, Yun-Ru Chen, and Chau-Hwang Lee, 2014, “Using optical profilometry to characterize cell membrane roughness influenced by Amyloid-beta 42 aggregates and electric fields”, Journal of Biomedical Optics, 19(1), 011009. (SCI)
  • Yu-Sheng Fang, Kuen-Jer Tsai, Yu-Jen Chang, Patricia Kao, Rima Woods, Pan-Hsien Kuo, Cheng-Chun Wu, Jhih-Ying Liao, Shih-Chieh Chou, Vinson Lin, Lee-Way Jin, Hanna S. Yuan, Irene H Cheng, Pang-Hsien Tu, and Yun-Ru Chen*, 2014, “Full-Length TDP-43 Forms Toxic Amyloid Oligomers that are Present in Frontotemporal Lobar Dementia-TDP Patients.”, Nature Communications, 5, 4824. (SCI)
  • Man Hoang Viet, Chun-Yu Chen, Chin-Kun Hu, Yun-Ru Chen*, and Mai Suan Li*., 2013, “Discovery of Dihydrochalcone as potential lead for Alzheimer's disease: in silico and in vitro study”, PLoS One, 8(11), e79151. (SCI)
  • Rong-Jie Chen, Wei-Wei Chang, Yu-Chun Lin, Pei-Lin Pheng, Yun-Ru Chen*, 2013, “Alzheimer’s Amyloid-β Oligomers Rescue Cellular Prion Protein Induced Tau Reduction via Fyn Pathways”, ACS Chemical Neuroscience, 4(9), 1287-1296. (SCI)
  • Yi-Ting Wang, Pan-Hsien Kuo, Chien-Hao Chiang, Jhe-Ruei Liang, Yun-Ru Chen, Shuying Wang, James C. K. Shen, and Hanna S. Yuan*., 2013, “The truncated C-terminal RRM domain of TDP-43 plays a key role in forming proteinaceous aggregates.”, J Biol. Chem., 288(13), 9049-9057. (SCI)
  • Winny Ariesandi, Chi-Fon Chang, Tseng-Erh Chen,Yun-Ru Chen*, 2013, “Temperature-dependent structural changes of Parkinson's alpha-synuclein reveal the role of pre-existing oligomers in alpha-synuclein fibrillization”, PLoS One, 8(1), e53487. (SCI)
  • Yi-Hung Liao, Yu-Jen Chang, Yuji Yoshiike, Yun-Chorng Chang*, and Yun-Ru Chen*, 2012, “Negatively charged gold nanoparticles inhibit Alzheimer's amyloid-beta fibrillization, induce fibril dissociation, and mitigate neurotoxicity”, SMALL, 8(23), 3631-3639. (SCI)
  • Wei-Ting Chen, Chen-Jee Hong, Ya-Tzu Lin, Wen-Han Chang, He-Ting Huang, Jhih-Ying Liao, Chih-Ya Cheng, Hsiu-Chih Liu, Yun-Ru Chen*, and Irene H Cheng *, 2012, “Amyloid-beta (Abeta) D7H mutation increases oligomeric Abeta42 and alters properties of Abeta-zinc/copper assemblies ”, PLos One, 7(4), e35807. (SCI)
  • Chun-Lun Ni, Hoi-Ping Shi, Kuo-Ging Lin, Hui-Ming Yu, and Yun-Ru Chen*, 2011, “Folding Stability of Amyloid-beta 40 Monomer is an Important Determinant of the Nucleation Phase in Fibrillization”, Faseb Journal, 25(4),1390-1401. (SCI)
  • Wei-Ting Chen, Yi-Hung Liao, Hui-Ming Yu, Irene H. Cheng, and Yun-Ru Chen*, 2011, “Distinct Effects of Zn2+, Cu2+, Fe3+, and Al3+ on Amyloid-beta Stability, Oligomerization, and Aggregation: Amyloid-beta Destabilization Promotes Annular Protofibril Formation”, Journal of Biological Chemistry, 286(11), 9646-9656. (SCI)
  • Ni-Shian Lin, John Ching-Hao Chao, Fang-Chieh Chou, Chi-Fon Chang, Yun-Ru Chen, Yu-Jen Chang, Shing-Jong Huang, Wei-Hsiang Tseng, and Jerry C. C. Chan, 2010, “Molecular Structure of Amyloid Fibrils Formed by Residues 127 to 147 of the Human Prion Protein”, Chemistry - A European Journal, 16(18), 5492-5499. (SCI)
  • Yuji Yoshiike, Ryoichi Minai, Yo Matsuo, Yun-Ru Chen, Tetsuya Kimura, Akihiko Takashima* , 2008, “Amyloid Oligomer Conformation in a Group of Natively Folded Proteins”, PLos ONE., 3(9), e3235. (SCI)
  • Yun-Ru Chen and Charles G. Glabe*, 2006, “Distinct Early Folding and Aggregation Properties of Alzheimer Amyloid-b Peptide Aβ40 and Aβ42: Stable Trimer or Tetramer Formation by Ab42”, J Biol. Chem, 281, 24414-24422. (SCI)
  • Yun-Ru Chen and A. Clay Clark*, 2006, “Substitutions of prolines examine their role in kinetic trap formation of the caspase recruitment domain (CARD) of RICK”, Protein Science, 15, 395-409. (SCI)
  • Yun-Ru Chen and A. Clay Clark*, 2004, “Kinetic traps in the folding/unfolding of procaspase-1 CARD Domain”, Protein Science, 13, 2196-2206. (SCI)
  • Yun-Ru Chen and A. Clay Clark*, 2003, “Equilibrium and Kinetic Folding of the α-Helical Greek Key Protein Domain: Caspase Recruitment Domain (CARD) of RICK”, Biochemistry, 42, 6310-6320. (SCI)
  • C. Pop, Y. R. Chen, B. Smith, K. Bose, B. Bobay, A. Tripathy, S. Franzen and A. C. Clark*, 2001, “Removal of the pro-domain does not affect the conformation of the procaspase-3 dimer”, Biochemistry, 40, 14224-14235. (SCI)